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Welcome to the Functional Genomics Plant Polyploid site

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Plant Material

Click on the image of Arabidopsis, Brassica, or corn to get more more information on the plant material used in the ABC collaboration

The Project

We are an NSF-funded project made of eight collaborators in research and teaching institutions. Our goal is to understand the regulatory mechanisms associated with polyploidy. Mounting evidence suggests that polyploidy is a major force for the evolution of plants and probably of chordates. It is now clear that a true understanding of plant genomes will require elucidating the short- and long-term impact of polyploidy on evolutionary events. The consequences of genome duplication on gene regulation and phenotypic variation are largely unknown. In the previous funding period we established three model systems and developed tools to investigate genomic and regulatory changes in polyploids. Our results, and those of others, have focused our attention on two major questions that, in our opinions, are the most critical for an understanding of polyploidy.

  • What mechanisms determine the fate of duplicated genes and genomes?
  • What is the basis of non-additive gene regulation?

Both these problems are tractable in the time scale of our experimental systems because events affecting gene regulation and genomic function are evident immediately following polyploidization. Yet, these events have long-term consequences and their elucidation is required to frame the effects of polyploidy in the light of evolution. The first question is being addressed by studying genomic interactions affecting fitness in neopolyploids. Using allelic variation in maize and Arabidopsis, we are examining the genetic architecture of fitness and heterosis. Furthermore, in Brassica we are examining the effects of genomic rearrangements on these characteristics. Based on our evidence, we propose that chromatin regulation plays a significant role. To test this hypothesis we will examine multiple levels of gene regulation including transcriptional and post-transcriptional regulation of duplicate loci in polyploids. The second question focuses on the surprising observation that duplicated genes in polyploids are frequently expressed in a non-additive fashion (not at midparental level). This unexpected aspect of gene expression could potentially explain mechanisms leading to sub-functionalization and novel phenotypes in polyploids. We are using enhancer-trap reporters to visualize the regulatory outcome of hybridization and polyploidization. Furthermore, the hypothesis that structural DNA and chromatin features of non-additively regulated genes are involved is being tested by extensive characterization of loci identified through transcriptional analysis.

Funding provided by the Plant Genome Program of the National Science Foundation

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